rs1971773
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_144681.3(CCDC42):c.*138G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 717,498 control chromosomes in the GnomAD database, including 48,714 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.32 ( 8660 hom., cov: 33)
Exomes 𝑓: 0.37 ( 40054 hom. )
Consequence
CCDC42
NM_144681.3 3_prime_UTR
NM_144681.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.34
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC42 | NM_144681.3 | c.*138G>A | 3_prime_UTR_variant | 7/7 | ENST00000293845.8 | ||
CCDC42 | NM_001158261.2 | c.*138G>A | 3_prime_UTR_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC42 | ENST00000293845.8 | c.*138G>A | 3_prime_UTR_variant | 7/7 | 2 | NM_144681.3 | P1 | ||
CCDC42 | ENST00000539522.2 | c.*138G>A | 3_prime_UTR_variant | 6/6 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.322 AC: 49021AN: 152052Hom.: 8656 Cov.: 33
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GnomAD4 exome AF: 0.366 AC: 206928AN: 565328Hom.: 40054 Cov.: 7 AF XY: 0.365 AC XY: 111138AN XY: 304182
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GnomAD4 genome ? AF: 0.322 AC: 49042AN: 152170Hom.: 8660 Cov.: 33 AF XY: 0.331 AC XY: 24629AN XY: 74378
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at